To prolong the life of eco-friendly alkali-activated slag-based (AAS) geopolymers, carbon nanotubes (CNTs) have been adopted as reinforcements due to their outstanding properties. However, the hydrophobic nature of CNTs poses challenges in establishing a strong interfacial compatibility with the hydrophilic calcium-aluminum-silicate-hydrate (C-A-S-H) gel, which plays a crucial role in determining the strength of these geopolymers. This disparity leads to inadequate interfacial adhesion between CNTs and C-A-S-H gel, primarily resulting in material failure at the interface of CNTs reinforced AAS geopolymers. Despite employing various surface modification techniques to address this issue, the precise impact of functional groups on the interfacial interaction at the nanoscale between CNTs and C-A-S-H gels remains uncertain. In this work, the atomistic-scale impact of functional groups on the interfacial properties between CNTs and C-A-S-H gels has been investigated. Compared to unmodified CNTs, CNTs functionalized with carboxyl groups exhibit a remarkable 16.9 % increase in the maximum pull stress during the pull-out process, whereas those functionalized with hydroxyl groups show a more modest 3.5 % improvement. Water molecules gradually desorb from the functionalized CNTs and re-adsorb onto the C-A-S-H structure during the pull-out process, which consumes energy. Functional groups amplify this effect by involving more water molecules in these dynamic processes during interface failure. These findings provide valuable theoretical guidance for optimizing the surface modification techniques of CNTs and underscore the untapped potential of CNTs in enhancing the performance of AAS geopolymer composites.